The present study analyses the spatio-temporal structuration of the molluscan fauna from four tidal channels of the Gulf of Gabès. A total of 26 stations were sampled at four seasons from March 2016 to January 2017, leading to the identification of 2695 individuals and 57 species. The species richness and abundances are higher in autumn than in other seasons. The fauna is dominated by seven species, three gastropods [Cerithium scabridum Philippi, 1848, Bittium reticulatum (da Costa, 1778) and Tricolia speciosa (Megerle von Mühfleld, 1824)] and four bivalves [Abra alba (W. Wood, 1802), Loripes orbiculatus Poli, 1791, Varicorbula gibba (Olivi, 1792) and Peronaea planata (Linnaeus, 1758)], which are characteristic of habitats with detritus accumulation and seagrass meadows. These dominant species are commonly recorded in lagoons and coastal shallow waters of the Mediterranean Sea. The structure of the molluscan fauna is linked to the location of tidal channels in the Gulf of Gabès. Abundances are lower in the Mimoun channel than in the other channels, especially the Maltine channel which shows a great accumulation of organic matter and high abundances of molluscs. Low abundances are found in high-energy hydrodynamic zones with gravel sediment; conversely, the presence of macrophytes (mainly in seagrass meadows) increases molluscan diversity. Comparisons with other sites in the shallow waters of the Tunisian coast and lagoons show that the taxonomic diversity of molluscs of the tidal channels of the Gulf of Gabès is equivalent to that reported elsewhere, but the abundance per m2 is among the lowest levels recorded here. Moreover, most of the dominant species found in the Gulf of Gabès tidal channel are reported as dominant in other studies covering the Mediterranean Sea. A distance-based redundancy analysis shows that depth, sediment type and the presence of marine phanerogams and filter-feeder bivalves on fine sands and gravels account for the structure of mollusc assemblages associated with each channel.